ISLAMABAD/BRUSSELS (Reuters) – NATO's chief expressed regret on Monday for the deaths of Pakistani soldiers last week and said he hoped Pakistan's border would reopen for NATO supplies to Afghanistan as soon as possible.

Angered by repeated attacks by NATO helicopters within its borders, Pakistan blocked one of the supply routes for NATO troops in Afghanistan after a strike killed three Pakistani soldiers in the western Kurram region.

“I expressed my regret for the incident last week in which Pakistani soldiers lost their lives,” Secretary-General Anders Fogh Rasmussen said after meeting Pakistani Foreign Minister Shah Mehmood Qureshi in Brussels.

“I expressed my hope the border will be open for supplies as soon as possible.”

The apology came after gunmen attacked a convoy of trucks taking goods to Western forces in Afghanistan on the outskirts of the Pakistani capital, killing three guards.

Pakistan has officially said the border has been closed for security reasons and the Taliban threat of more attacks will likely prolong the closure of the vital supply route -- now in its fifth day -- and further strain ties with ally Washington, which has long demanded Pakistan crack down on militants.

About half of all non-lethal supplies for western forces in land-locked Afghanistan pass through Pakistan, giving Pakistan considerable leverage over the United States, which needs Pakistan for help in containing the insurgency in Afghanistan.

“Efforts are underway to resolve this issue, but there is a lot of anger in Pakistan about the border incursion,” a senior Pakistani government official told Reuters.

ISAF spokesman Major Joel Harper told Reuters in Kabul that the border closure wouldn't impact the mission, but that the supply lines are “an important element of the Pakistani economy. It's important to our logistics stocks.”

The closures would force more supplies through NATO's northern supply route through Russia and the central Asian republics, he said.

“NATO authorities have all along anticipated disruptions in the supply chain and have been stockpiling supplies in advance,” said Kamran Bokhari, South Asia director at STRATFOR global intelligence.

Andrew Exum, a fellow with the Center for a New American Security and former adviser on Gen. Stanley McChrystal's assessment team in Afghanistan, said the closures mattered little tactically.

“Even though it's painful it doesn't cripple the mission,” he said. “The larger strategic issue is that we're seeing a period of rising public tension between the United States and Pakistan.”

“It's clear the Pakistanis are frustrated with the United States,” he continued. “It's clear the Pakistanis are frustrated with the drone strikes in Pakistan. What I don't think the Pakistanis understand is how frustrated the Americans and the American public are with the Pakistanis.”

Despite its anger, Pakistan can't afford to long antagonize an ally that provides $2 billion in military aid a year -- aid vital for Pakistan's own fight against militants, analysts say.

“There has to be some solution and I think there will be one. But there is an anger and you have to address it,” a Pakistani security official said.

Officials at the U.S. embassy in Islamabad said despite the protests by Pakistan and the closing of the border, cooperation in flood relief missions and security assistance continues.

Rasmussen said the killing of the three Pakistani soldiers was unintended and showed the need to improve coordination between the NATO and the Pakistani military. He said a joint investigation was under way.

“It is important we step up our cooperation,” he said.

That cooperation could be slow in coming, however, because a stepped up campaign of drone strikes has infuriated many Pakistanis and made it harder for the government to cooperate with the United States.

The strikes preceded warnings by Britain and the United States of an increased risk of terrorist attacks in Europe, with Washington saying al Qaeda might target transport infrastructure.

Late on Monday, two missiles from a suspected CIA drone struck a mosque in Mirali in North Waziristan, about 20 km east of the main town of Miranshah, intelligence officials said. Three people were killed.